Contacts of the strand formed by residues 480 - 488 (chain A) in PDB entry 1NRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A LEU 3.8 0.3 - - - +
476A CYS* 3.2 2.8 - - - -
477A HIS* 2.9 32.6 + - - +
478A HIS* 4.0 9.0 - - + +
479A GLN* 1.3 84.9 - - - +
481A ILE* 1.3 63.9 + - - +
482A LYS* 3.9 28.2 + - - +
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A HIS* 3.5 42.2 - - + +
449A ILE* 3.2 30.5 - - + -
450A LYS* 3.5 34.8 - - - +
454A LEU* 3.8 16.4 - - + -
474A THR* 3.6 23.1 - - + -
475A LEU 3.4 5.4 - - - +
476A CYS* 4.2 4.0 - - + -
479A GLN 4.2 1.1 + - - +
480A LYS* 1.3 73.7 - - - +
482A LYS* 1.3 74.5 + - - +
483A ASN* 4.8 1.2 + - - -
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Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU 3.7 0.9 - - - +
474A THR* 3.4 3.8 - - - +
475A LEU 2.7 38.3 + - - +
477A HIS* 6.0 0.7 - - + +
480A LYS* 4.2 29.9 - - - +
481A ILE* 1.3 84.3 + - - +
483A ASN* 1.3 65.5 + - - +
484A PHE* 3.7 26.1 - - + -
524A PRO* 4.7 15.9 - - + -
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ARG* 3.8 19.2 - - - +
446A HIS* 2.9 30.8 + - - -
462A ARG* 3.0 16.3 + - - +
472A VAL* 4.1 8.5 - - + -
473A LEU 3.2 3.6 - - - +
474A THR* 2.6 32.6 + - - +
481A ILE 4.8 0.8 + - - -
482A LYS* 1.3 79.2 - - - +
484A PHE* 1.3 69.4 + - - +
485A GLN* 4.0 9.1 - - + +
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A VAL* 3.4 4.1 - - - -
473A LEU* 2.8 59.0 + - + +
475A LEU* 4.9 5.8 - - + -
482A LYS* 3.7 30.7 - - + -
483A ASN* 1.3 79.6 - - - +
485A GLN* 1.3 66.3 + - - +
486A ILE* 3.6 1.2 + - - +
499A LEU* 4.3 20.0 - - + +
522A VAL* 4.3 22.0 - - + -
523A LEU* 3.7 33.7 - - + -
524A PRO* 3.8 22.0 - - + -
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Residues in contact with GLN 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A PHE 3.7 6.7 - - - +
472A VAL* 4.6 10.8 - - + +
483A ASN* 4.0 8.2 - - + +
484A PHE* 1.3 79.6 - - - +
486A ILE* 1.3 61.2 + - - +
487A LEU* 3.7 26.3 + - + +
498A SER 3.6 2.1 - - - +
499A LEU* 3.3 22.5 + - - +
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Residues in contact with ILE 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A LEU* 3.8 28.7 - - + -
470A ALA* 3.5 5.7 - - - +
471A PHE* 2.8 43.7 + - + +
473A LEU* 4.1 19.7 - - + +
484A PHE 4.2 5.2 - - - +
485A GLN* 1.3 72.6 - - - +
487A LEU* 1.3 61.9 + - - +
488A PRO* 4.3 0.2 - - - +
497A PHE* 3.8 28.8 - - + -
498A SER 3.5 5.8 - - - +
499A LEU* 4.1 15.9 - - + -
509A LEU* 3.9 14.6 - - + -
512A LEU* 3.9 25.4 - - + -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASN* 4.8 7.2 - - + +
470A ALA* 3.9 22.2 - - + -
485A GLN* 4.2 26.2 - - + +
486A ILE* 1.3 75.6 - - - +
488A PRO* 1.3 74.0 - - + +
489A CYS* 5.1 1.0 - - - +
496A PHE 3.8 0.3 - - - +
497A PHE* 3.4 4.7 - - - -
498A SER* 3.0 33.5 + - - +
501A ASP* 5.3 8.7 - - - +
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Residues in contact with PRO 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASN* 4.9 6.7 - - - +
469A LYS* 3.5 40.8 - - + +
470A ALA* 4.3 4.7 - - + -
486A ILE 4.3 1.3 - - - +
487A LEU* 1.3 92.1 - - + +
489A CYS* 1.3 67.4 + - - +
495A THR* 4.0 12.8 - - + -
496A PHE 3.2 7.6 - - - +
497A PHE* 3.9 19.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il